Atomistic studies of <110] screw dislocation core structures and glide in γ-TiAl

The core structure of <110] superdislocations in L10 TiAl was investigated with a view to clarifying their dissociation abilities and the mechanisms by which they may become sessile by self-locking. A detailed knowledge of the fine structure of dislocations is essential in analysing the origin of the various deformation features. Atomistic simulation of the core structure and glide of the screw <110] superdislocation was carried out using a bond order potential for ?-TiAl. The core structure of the screw <110] superdislocation was examined, starting with initial unrelaxed configurations corresponding to various dislocation dissociations discussed in the literature. The superdislocation was found to possess in the screw orientation either planar (glissile) or non-planar (sessile) core structures. The response of the core configurations to externally applied shear stress was studied. Some implications were considered of the dissociated configurations and their response to externally applied stress on dislocation dynamics, including the issue of dislocation decomposition, the mechanism of locking and the orientation dependence of the dislocation substructure observed in single-phase ?-TiAl. An unexpectedly rich and complex set of candidate core structures, both planar and non-planar, was found, the cores of which may transform under applied stress with consequent violation of Schmid's law.

Atomistic studies of interactions between the dominant lattice dislocations and γ/γ-lamellar boundaries in lamellar γ-TiAl

This paper reports on atomistic simulations of the interactions between the dominant lattice dislocations in ?-TiAl (<1 0 1] superdislocations) with all three kinds of ?/?-lamellar boundaries in polysynthetically twinned (PST) TiAl. The purpose of this study is to clarify the early stage of lamellar boundary controlled plastic deformation in PST TiAl. The interatomic interactions in our simulations are described by a bond order potential for L10-TiAl which provides a proper quantum mechanical description of the bonding. We are interested in the dislocation core geometries that the lattice produces in proximity to lamellar boundaries and the way in which these cores are affected by the elastic and atomistic effects of dislocation-lamellar boundary interaction. We study the way in which the interfaces affect the activation of ordinary dislocation and superdislocation slip inside the ?-lamellae and transfer of plastic deformation across lamellar boundaries. We find three new phenomena in the atomic-scale plasticity of PST TiAl, particularly due to elastic and atomic mismatch associated with the 60° and 120° ?/?-interfaces: (i) two new roles of the ?/?-interfaces, i.e. decomposition of superdislocations within 120° and 60° interfaces and subsequent detachment of a single ordinary dislocation and (ii) blocking of ordinary dislocations by 60° and 120° interfaces resulting in the emission of a twinning dislocation.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

Is the pinning of ordinary dislocations in γ-TiAl intrinsic or extrinsic in nature? A combined atomistic and kinetic Monte Carlo approach

We address the question of the observed pinning of 1/2

Thermodynamic properties and atomistic structure of the dry amorphous silica surface from a reactive force field model

A force field model of the Keating type supplemented by rules to break, form, and interchange bonds is applied to investigate thermodynamic and structural properties of the amorphous SiO2 surface. A simulated quench from the liquid phase has been carried out for a silica sample made of 3888 silicon and 7776 oxygen atoms arranged on a slab similar to 40 angstrom thick, periodically repeated along two directions. The quench results into an amorphous sample, exposing two parallel square surfaces of similar to 42 nm(2) area each. Thermal averages computed during the quench allow us to determine the surface thermodynamic properties as a function of temperature. The surface tension turns out to be gamma=310 +/- 20 erg/cm(2) at room temperature and gamma=270 +/- 30 at T=2000 K, in fair agreement with available experimental estimates. The entropy contribution Ts-s to the surface tension is relatively low at all temperatures, representing at most similar to 20% of the surface energy. Almost without exceptions, Si atoms are fourfold coordinated and oxygen atoms are twofold coordinated. Twofold and threefold rings appear only at low concentration and are preferentially found in proximity of the surface. Above the glass temperature T-g=1660 +/- 50 K, the mobility of surface atoms is, as expected, slightly higher than that of bulk atoms. The computation of the height-height correlation function shows that the silica surface is rough in the equilibrium and undercooled liquid phase, becoming smooth below the glass temperature T-g.

Combined studies of DFT atomistic modelling and in situ FTIR spectroscopy on surface oxidants and CO oxidation at Ru electrodes

We report the combined studies of density functional theory (DFT) calculations and electrochemical in situ FTIR spectroscopy on surface oxidants and mechanisms of CO oxidation at the Ru(0001) electrodes. It is shown that CO can co-adsorb with both O and OH species at lower potential region where a low coverage of the (2 x 2)-O/OH adlayer formed; the oxidation of CO adsorbates takes place at higher potentials where a high coverage of the (1 x 1)-O/OH adlayer formed. Surface O species are not the active oxidants under all coverages studied, due to the high reaction barriers between CO and O (>1 eV). However, surface OH species with higher coverage are identified as the active oxidants, and CO oxidation takes place via a two-steps' mechanism of CO + 3OH -> COOH + 2OH -> CO2 + H2O + OH, in which three nearby OH species are involved in the CO2 formation: CO reacts with OH, forming COOH; COOH then transfers the H to a nearby OH to form H2O and CO2, at the same time, another H in the H2O transfers to a nearby OH to form a weak adsorbed H2O and a new OH. The reaction barrier of these processes is reduced significantly to around 0.50 eV. These new results not only provide an insight into surface active oxidants on Ru, which is directly relevant to fuel cell catalysis, but also reveals the extra complexity of catalytic reactions taking place at solid/liquid electrochemical interface in comparison to the relatively simpler ones at solid/gas phase. 

Atomistic investigation on the structure-property relationship during thermal spray nanoparticle impact

During thermal spraying, hot particles impact on a colder substrate. This interaction of crystalline copper nanoparticles and copper substrate is modelled, using MD simulation. The quantitative results of the impacts at different velocities and temperatures are evaluated using a newly defined flattening aspect ratio. This ratio between the maximum diameter after the impact and the height of the splat increases with increasing Reynolds numbers until a critical value is reached. At higher Reynolds numbers the flattening aspect ratio decreases again, as the kinetic energy of the particle leads to increasing substrate temperature and, therefore, decreases the substrate resistance. Thus, the particle penetrates into the substrate and deforms less.

Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure. (C) 2001 American Institute of Physics.

Structural motifs of cholesterol nanoparticles

The growth sequence of gas-phase cholesterol clusters (Ch(N)) with up to N=36 molecules has been investigated by atomistic simulation based on an empirical force field model. The results of long annealings from high temperature show that the geometric motifs characterizing the structure of pure cholesterol crystals already appear in nanometric aggregates. In all clusters molecules tend to align along a common direction. For cluster sizes above the smallest ones, dispersion interactions among the hydrocarbon body and tails of cholesterol cooperate with hydrogen bonding to give rise to a bilayer structure. Analysis of snapshots from the annealing shows that the condensation of hydrogen bonds into a connected network of rings and chains is an important step in the self-organization of cholesterol clusters. The effect of solvation on the equilibrium properties of medium-size aggregates is investigated by short molecular dynamics simulations for the N=30 and N=40 clusters in water at near ambient conditions and in supercritical carbon dioxide at T=400 K.